Abstract
Original language | English (US) |
---|---|
Pages (from-to) | 3258-3268 |
Number of pages | 11 |
Journal | Evolution |
Volume | 63 |
Issue number | 12 |
DOIs | |
State | Published - Dec 2009 |
Fingerprint
Dive into the research topics of 'Size-correction and principal components for interspecific comparative studies'. Together they form a unique fingerprint.Cite this
- APA
- Author
- BIBTEX
- Harvard
- Standard
- RIS
- Vancouver
}
In: Evolution, Vol. 63, No. 12, 12.2009, p. 3258-3268.
Research output: Contribution to journal › Research Article › peer-review
TY - JOUR
T1 - Size-correction and principal components for interspecific comparative studies
AU - Revell, L.J.
N1 - Cited By :289 Export Date: 17 April 2018 CODEN: EVOLA Correspondence Address: Revell, L. J.; National Evolutionary Synthesis Center, 2024 W. Main St. A200, Durham, NC 27705, United States; email: [email protected] References: Ackerly, D.D., Donoghue, M.J., Leaf size, sapling allometry, and Corner's rules: Phylogeny and correlated evolution in maples (Acer) (1998) Am. Nat., 152, pp. 767-791; Andrews, C.B., MacKenzie, S.A., Gregory, T.R., Genome size and wing parameters in passerine birds (2009) Proc. R. Soc. Lond. B, 276, pp. 55-61; Blomberg, S.P., Garland Jr., T., Tempo and mode in evolution: Phylogenetic inertia, adaptation and comparative methods (2002) J. Evol. Biol., 15, pp. 899-910; Blomberg, S.P., Garland Jr., T., Ives, A.R., Testing for phylogenetic signal in comparative data: Behavioral traits are more labile (2003) Evolution, 57, pp. 717-745; Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) Am. Nat., 164, pp. 683-695; Butler, M.A., Schoener, T.W., Losos, J.B., The relationship between sexual size dimorphism and habitat use in Greater Antillean Anolis lizards (2000) Evolution, 54, pp. 259-272; Cheverud, J.M., Dow, M.M., Leutenegger, W., The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates (1985) Evolution, 39, pp. 1335-1351; Clobert, J., Garland Jr., T., Barbault, R., The evolution of demographic tactics in lizards: A test of some hypotheses concerning life history evolution (1998) J. Evol. Biol., 11, pp. 329-364; Felsenstein, J., Phylogenies and the comparative method (1985) Am. Nat., 125, pp. 1-15; Felsenstein, J., Phylogenies and quantitative characters (1988) Ann. Rev. Ecol. Syst., 19, pp. 445-471; Freckleton, R.P., On the misuse of residuals in ecology: Regression of residuals vs. multiple regression (2002) J. Anim. Ecol., 71, pp. 542-545; Freckleton, R.P., The seven deadly sins of comparative analysis (2009) J. Evol. Biol., 22, pp. 1367-1375; Freckleton, R.P., Harvey, P.H., Pagel, M., Phylogenetic analysis and comparative data: A test and review of evidence (2002) Am. Nat., 160, pp. 712-726; García-Berthou, E., On the misuse of residuals in ecology: Testing regression residuals vs. the analysis of covariance (2001) J. Anim. Ecol., 70, pp. 708-711; Garland Jr., T., Ives, A.R., Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods (2000) Am. Nat., 155, pp. 346-364; Garland Jr., T., Harvey, P.H., Ives, A.R., Procedures for the analysis of comparative data using phylogenetically independent contrasts (1992) Syst. Biol., 41, pp. 18-32; Garland Jr., T., Dickerman, A.W., Janis, C.M., Jones, J.A., Phylogenetic analysis of covariance by computer simulation (1993) Systematic Biology, 42 (3), pp. 265-292; Garland Jr., T., Bennett, A.F., Rezende, E.L., Phylogenetic approaches in comparative physiology (2005) J. Exp. Biol., 208, pp. 3015-3035; Glossip, D., Losos, J.B., Ecological correlates of number of subdigital lamellae in anoles (1997) Herpetologica, 53, pp. 192-199; Gould, S.J., Allometry and size in ontogeny and phylogeny (1966) Biol. Rev., 41, pp. 587-638; Grafen, A., The phylogenetic regression (1989) Phil. Trans. R. Soc. Lond. B, 326, pp. 119-157; Hansen, T.F., Stabilizing selection and the comparative analysis of adaptation (1997) Evolution, 51, pp. 1341-1351; Hansen, T.F., Martins, E.P., Translating between microevolutionary process and macroevolutionary patterns: The correlation structure of interspecific data (1996) Evolution, 50, pp. 1404-1417. , and; Hansen, T.F., Pienaar, J., Orzack, S.H., A comparative method for studying adaptation to a randomly evolving environment (2008) Evolution, 62, pp. 1965-1977. , and; Harvey, P.H., Pagel, M.D., (1991) The Comparative Method in Evolutionary Biology., , and. Oxford Univ. Press. Oxford, UK; Hulsey, C.D., Mims, M.C., Streelman, J.T., Do constructional constraints influence cichlid craniofacial diversification? (2007) Proc. R. Soc. Lond. B, 274, pp. 1867-1875. , and; Humphries, J.M., Bookstein, F.L., Chernoff, B., Smith, G.R., Elder, R.L., Poss, S.G., Multivariate discrimination by shape in relation to size (1981) Syst. Zool., 30, pp. 291-308. , and; Jolicoeur, P., Pirlot, P., Baron, G., Stephan, H., Brain structure and correlation patterns in Insectivora, Chiroptera, and Primates (1984) Syst. Zool., 33, pp. 14-29. , and; Lavin, S.R., Karasov, W.H., Ives, A.R., Middleton, K.M., Garland Jr., T., Morphometrics of the avian small intestine compared with that of nonflying mammals: A phylogenetic approach (2008) Physiol. Biochem. Zool., 81, pp. 526-550. , and; Manly, B.F.J., (2005) Multivariate Statistical Methods: A Primer, 3rd Edn., , Chapman & Hall / CRC. Boca Raton, FL; Martins, E.P., Estimating the rate of phenotypic evolution from comparative data (1994) Am. Nat., 144, pp. 193-209; Martins, E.P., Garland Jr., T., Phylogenetic analyses of the correlated evolution of continuous characters: A simulation study (1991) Evolution, 45, pp. 534-557. , and; Martins, E.P., Hansen, T.F., Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data (1997) Am. Nat., 149, pp. 646-667. , and; McCoy, M.W., Bolker, B.J., Osenberg, C.W., Miner, B.G., Vonesh, J.R., Size correction: Comparing morphological traits among populations and environments (2006) Oecologia, 148, pp. 547-554. , and; Nunn, C.L., Barton, R.A., Comparative methods for studying primate adaptation and allometry (2001) Evol. Anthropol., 10, pp. 81-98. , and; O'Meara, B.C., Ané, C., Sanderson, M.J., Wainwright, P.C., Testing for different rates of continuous trait evolution using likelihood (2006) Evolution, 60, pp. 922-933. , and; Pagel, M., Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters (1994) Proc. R. Soc. Lond. B, 255, pp. 37-45; Pagel, M., Inferring the historical patterns of biological evolution (1999) Nature, 401, pp. 877-884; Paradis, E., (2006) Analysis of Phylogenetics and Evolution with R., , Springer. New York, NY; Paradis, E., Claude, J., Strimmer, K., APE: Analyses of phylogenetics and evolution in R language (2004) Bioinformatics, 20, pp. 289-290. , and; Pontzer, H., Kamilar, J.M., Great ranging associated with greater reproductive investment in mammals (2009) Proc. Natl. Acad. Sci. USA, 106, pp. 192-196. , and; Price, T., Correlated evolution and independent contrasts (1997) Phil. Trans. R. Soc. Lond. B, 352, pp. 519-529; (2008) R: A Language and Environment for Statistical Computing., , R Development Core Team. R Foundation for Statistical Computing. Vienna, Austria; Rencher, A.C., (2002) Methods of Multivariate Analysis, 2nd Edn., , John Wiley & Sons. Hoboken, NJ; Rencher, A.C., Schaalje, G.B., (2008) Linear Models in Statistics, 2nd Edn., , and. John Wiley & Sons. Hoboken, NJ; Revell, L.J., Testing the genetic constraint hypothesis in a phylogenetic context: A simulation study (2007) Evolution, 61, pp. 2720-2727; Revell, L.J., On the analysis of evolutionary change along single branches in a phylogeny (2008) Am. Nat., 172, pp. 140-147; Revell, L.J., Collar, D.C., Phylogenetic analysis of the evolutionary correlation using likelihood (2009) Evolution, 63, pp. 1090-1100. , and; Revell, L.J., Harmon, L.J., Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters (2008) Evol. Ecol. Res., 10, pp. 311-321. , and; Revell, L.J., Harrison, A.S., PCCA: A program for phylogenetic canonical correlation analysis (2008) Bioinformatics, 24, pp. 1018-1020. , and; Revell, L.J., Harmon, L.J., Langerhans, R.B., Kolbe, J.J., A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the neotropical lizard Anolis cristatellus (2007) Evol. Ecol. Res., 9, pp. 261-282. , and; Revell, L.J., Harmon, L.J., Collar, D.C., Phylogenetic signal, evolutionary process, and rate (2008) Syst. Biol., 57, pp. 591-601. , and; Rohlf, F.J., Comparative methods for the analysis of continuous variables: Geometric interpretations (2001) Evolution, 55, pp. 2143-2160; Rohlf, F.J., A comment on phylogenetic correction (2006) Evolution, 60, pp. 1509-1515; Rohlf, F.J., Bookstein, F.L., A comment on shearing as a method for "size correction" (1987) Syst. Zool., 36, pp. 356-367. , and; Schluter, D., Adaptive radiation along genetic lines of least resistance (1996) Evolution, 50, pp. 1766-1774; Schluter, D., Price, T., Mooers A.Ø, Ludwig, D., Likelihood of ancestor states in adaptive radiation (1997) Evolution, 51, pp. 1699-1711. , and; Matlab: The language of technical computing (R2006a) (2006) The MathWorks Inc., , The Mathworks. Natick, MA
PY - 2009/12
Y1 - 2009/12
N2 - Phylogenetic methods for the analysis of species data are widely used in evolutionary studies. However, preliminary data transformations and data reduction procedures (such as a size-correction and principal components analysis, PCA) are often performed without first correcting for nonindependence among the observations for species. In the present short comment and attached R and MATLAB code, I provide an overview of statistically correct procedures for phylogenetic size-correction and PCA. I also show that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in our statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. This means that ignoring phylogeny during preliminary data transformations can possibly lead to spurious results in phylogenetic statistical analyses of species data. © 2009 The Society for the Study of Evolution.
AB - Phylogenetic methods for the analysis of species data are widely used in evolutionary studies. However, preliminary data transformations and data reduction procedures (such as a size-correction and principal components analysis, PCA) are often performed without first correcting for nonindependence among the observations for species. In the present short comment and attached R and MATLAB code, I provide an overview of statistically correct procedures for phylogenetic size-correction and PCA. I also show that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in our statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. This means that ignoring phylogeny during preliminary data transformations can possibly lead to spurious results in phylogenetic statistical analyses of species data. © 2009 The Society for the Study of Evolution.
U2 - 10.1111/j.1558-5646.2009.00804.x
DO - 10.1111/j.1558-5646.2009.00804.x
M3 - Research Article
SN - 0014-3820
VL - 63
SP - 3258
EP - 3268
JO - Evolution
JF - Evolution
IS - 12
ER -